The defeat, a third of the season for the West Javan club, increases the pressure on coach Djadjang Nurdjaman, with Persib having now won just one of their last six league games. Both teams starting brightly. After 14 minutes, Carlton Cole made his first appearance since early May as the former England striker came off the bench to replace the injured Sergio van Dijk.
PSM could return to the summit with a win at home to Borneo on Monday.
In contrast to Persib's poor form, Persija are climbing the table and moved into fifth with a fourth successive win while a fourth goal of the season from Mohamed Sissoko helped Mitra Kukar into sixth.
The former Liverpool and Juventus attacker grabbed the second in a 3-1 win at home to Gresik United.